EDGE CT: NSF-BSF: Developing Functional Genomics Tools for Emerging Extremophyte Models

EDGE CT：NSF-BSF：为新兴极端植物模型开发功能基因组学工具

• 批准号: 1923589
• 负责人: Maheshi Dassanayake
• 金额: $ 100万
• 依托单位: Louisiana State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-10-01 至 2024-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1923589&HistoricalAwards=false
• 关键词: EDGE; CT; NSF; BSF; Developing

At a time when food security is challenged by diminishing freshwater resources and other environmental stresses that threaten modern agriculture, developing crops better adapted for stresses such as drought, cold, high heat, or saline-, toxic- and nutrient-poor soils is imperative. Plants that grow in naturally harsh environments present novel genetic resources for understanding their adaptations to multiple environmental stresses. Recent advances in genomic sciences enable the use of such wild species to identify unique gene functions that can be introduced to elite crop cultivars to help meet global agricultural needs. The goal of this project is to develop a molecular toolkit for two such wild plants that can be premier models for investigating how plants tolerate environmental stresses without significant yield losses, and how such traits can be integrated successfully into current crops. Project aims include developing methods to detect genes controlling these traits in the wild plants, targeting specific gene products to uesful tissue or cell types, and effectively monitoring gene function as an essential step to assessing the suitability of transferring these gene functions from a wild plant to a crop. This project will also provide training to graduate students and research scientists to use these new tools, and aims to inspire the next generation of plant researchers from K-12 through undergraduate students to look for genetic innovations yet to be discovered in wild plants.Deducing genome to phenome functional relationships is among the predominant goals of biological research, yet a large gap exists in our understanding of how plants adapt to environmental stress. Extremophytes are unique in their biology and exhibit many, naturally-selected adaptations to stresses, thus showing great promise for understanding genetic mechanisms to develop crops better adapted to varying environments. Two emerging extremophyte models, Schrenkiella parvula and Eutrema salsugineum, grow remarkably well under multiple environmental stresses compared to the model plant, Arabidopsis thaliana and most crops. Despite the availability of high-quality genomes for these extremophytes, their use in basic research is constrained by a lack of functional genomic tools and inadequate analytical infrastructure capable of integrating different data types. The goal is to develop functional genomics tools to enable the wider use of extremophytes for discovering genetic mechanisms for stress adaptation. Methods will be developed to improve transformation efficiency and targeted manipulation of the extremophyte genomes. The project will create tools to enable investigation of cell-type specific gene functions via single cell transcriptomics and the development of genetically encoded biosensors and provide a computational platform to study extremophyte gene functions. The entire team of investigators will be committed to a number of activities including workshops organized at international and regional plant science meetings and production of detailed online tutorials, to provide training and increase awareness of the resources generated in this project. The work also includes timely dissemination of the resources developed, as well as integrated educational outreach activities.This award is co-funded by the Enabling Discovery through GEnomic tools (EDGE) Program and the Plant Genome Research Program (PGRP) in the Division of Integrated Organismal SystemsThis award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

在粮食安全受到淡水资源减少和其他环境压力威胁现代农业的挑战之际，开发更好地适应干旱、寒冷、高温或盐碱、有毒和营养不良土壤等压力的作物势在必行。在自然恶劣环境中生长的植物为了解其对多种环境胁迫的适应提供了新的遗传资源。基因组科学的最新进展使得能够利用这些野生物种来鉴定独特的基因功能，这些基因功能可以引入到优良作物栽培品种中，以帮助满足全球农业需求。该项目的目标是为两种这样的野生植物开发一个分子工具包，它们可以成为研究植物如何在不造成重大产量损失的情况下耐受环境胁迫的首要模型，以及这些性状如何成功地整合到当前作物中。项目目标包括开发方法来检测野生植物中控制这些性状的基因，将特定的基因产物靶向有用的组织或细胞类型，并有效地监测基因功能，作为评估将这些基因功能从野生植物转移到作物的合适性的重要步骤。该项目还将为研究生和研究科学家提供使用这些新工具的培训，旨在激励下一代植物研究人员从K-12到本科生寻找尚未在野生植物中发现的遗传创新。推导基因组与表型组的功能关系是生物学研究的主要目标之一，然而，我们对植物如何适应环境压力的理解存在很大的差距。极端植物在其生物学上是独特的，并表现出许多自然选择的适应压力，从而显示出很大的希望，了解遗传机制，以开发更好地适应不同环境的作物。与模式植物拟南芥和大多数农作物相比，两种新兴的极端植物模式，小施仁克氏菌和盐生杜仲在多种环境胁迫下生长得非常好。尽管这些极端植物的高质量的基因组的可用性，它们在基础研究中的使用受到缺乏功能基因组工具和能够整合不同数据类型的分析基础设施不足的限制。其目标是开发功能基因组学工具，以便更广泛地利用极端植物来发现适应压力的遗传机制。将开发方法来提高极端植物基因组的转化效率和靶向操作。该项目将创建工具，通过单细胞转录组学和遗传编码生物传感器的开发来研究细胞类型特定的基因功能，并提供研究极端植物基因功能的计算平台。整个调查团队将致力于开展一系列活动，包括在国际和区域植物科学会议上组织的研讨会，以及制作详细的在线教程，以提供培训并提高对该项目所产生资源的认识。这项工作还包括及时传播所开发的资源，该奖项由通过基因组工具进行发现（EDGE）计划和植物基因组研究计划（PGRP）共同资助。综合生物系统部门该奖项反映了NSF的法定使命，并通过利用基金会的知识价值和更广泛的评估被认为值得支持影响审查标准。

项目成果

Living with high potassium: Balance between nutrient acquisition and K-induced salt stress signaling

高钾生活：营养获取与钾诱导的盐胁迫信号之间的平衡

• DOI: 10.1093/plphys/kiac564
• 发表时间: 2022
• 期刊: Plant Physiology
• 影响因子: 7.4
• 作者: Pantha, Pramod;Oh, Dong-Ha;Longstreth, David;Dassanayake, Maheshi
• 通讯作者: Dassanayake, Maheshi

Positive Selection and Heat-Response Transcriptomes Reveal Adaptive Features of the Arabidopsis Desert Relative, Anastatica hierochuntica

正选择和热响应转录组揭示了拟南芥沙漠近缘植物Anastatica hierochuntica的适应性特征

• 发表时间: 2021
• 期刊: bioRxiv
• 作者: Eshela, Gil;Duppena, Nick;Wang, Guannan;Oh, Dong-Ha;Kazachkova, Yana;Herzyk, Pawel;Amtmann, Anna;Gordon, Michal;Chalifa-Caspi, Vered;Oscar, Michelle Arland
• 通讯作者: Oscar, Michelle Arland

A conserved gene regulatory network controls root epidermal cell patterning in superrosid species

保守的基因调控网络控制超级玫瑰物种的根表皮细胞模式

• DOI: 10.1111/nph.18885
• 发表时间: 2023
• 期刊: New Phytologist
• 影响因子: 9.4
• 作者: Zhu, Yan;Schiefelbein, John
• 通讯作者: Schiefelbein, John

Alternative splicing preferentially increases transcript diversity associated with stress responses in the extremophyte Schrenkiella parvula

• DOI: 10.1101/2022.10.13.512046
• 发表时间: 2022-10
• 期刊: bioRxiv
• 作者: Chathura Wijesinghege;Kieu-Nga Tran;M. Dassanayake

Delayed leaf greening involves a major shift in the expression of cytosolic and mitochondrial ribosomes to plastid ribosomes in the highly phosphorus-use-efficient Hakea prostrata (Proteaceae)

• DOI: 10.1007/s11104-023-06275-1
• 发表时间: 2023-09
• 期刊: Plant and Soil
• 影响因子: 4.9
• 作者: Toby Bird;B. J. Nestor;P. Bayer;Guannan Wang;A. Ilyasova;Clément E Gille;Bryce E. H. Soraru;Kosala Ranathunge;A. Severn-Ellis;Ricarda Jost;W. Scheible;M. Dassanayake;Jacqueline Batley;D. Edwards;Hans Lambers;P. Finnegan